other · Figshare · 2015
Parameter optimization.
Kyuin Hwang (409161), Jeongsu Oh (409162), Tae-Kyung Kim (248173), Byung Kwon Kim (409163), Dong Su Yu (409164), Bo Kyeng Hou (409165), Gustavo Caetano-Anollés (65405), Soon Gyu Hong (409166), Kyung Mo Kim (409167)
Cited by 0Open access
Abstract
<p>We simulated three variable regions of the 454–HMP dataset (V1–3, V3–5, and V6–9) to determine optimal sizes of <i>k</i>-mer and random sample. (A) From each region, 10 K reads were randomly sampled 10 times and NW distances calculated. <i>k</i>-mer distances between the pairs of the 10 K reads were calculated for each of <i>k</i>-mer sizes ranging from 3 to 15. The extent of linear regression between the two distance variables was plotted using the mean (upper <i>x</i> axis) and standard deviation (lower <i>x</i> axis) of the square of the Person product-moment correlation coefficients (R-Square) at every point of the <i>k</i>-mer sizes. (B) For individual 16S regions, we randomly sampled sequences of 100 to 2,000 reads in increments of 100 reads. The <i>k</i>-mer and NW distances were calculated for all possible sequence pairs at every point of the random sample sizes. The random sampling followed by the distance calculation was repeated 10 times. For ten random samples per sample size, the mean (upper <i>x</i> axis) and standard deviation (lower <i>x</i> axis) of R-Square were calculated and displayed.</p>
Cite this paper
(409161), K. H., (409162), J. O., (248173), T.-K. K., (409163), B. K. K., (409164), D. S. Y., (409165), B. K. H., (65405), G. C.-A., (409166), S. G. H., & (409167), K. M. K. (2015). Parameter optimization. Figshare. https://doi.org/10.1371/journal.pone.0062623.g003
(409161), Kyuin Hwang, et al. “Parameter optimization.” Figshare, 2015, https://doi.org/10.1371/journal.pone.0062623.g003.
(409161), Kyuin Hwang, Jeongsu Oh (409162), Tae-Kyung Kim (248173), Byung Kwon Kim (409163), Dong Su Yu (409164), Bo Kyeng Hou (409165), Gustavo Caetano-Anollés (65405), Soon Gyu Hong (409166), and Kyung Mo Kim (409167). 2015. “Parameter optimization.” Figshare. https://doi.org/10.1371/journal.pone.0062623.g003.
(409161), K.H. et al. (2015) ‘Parameter optimization’, Figshare. Available at: https://doi.org/10.1371/journal.pone.0062623.g003.
@misc{4091612015parameter,
title = {{Parameter optimization.}},
author = {(409161), Kyuin Hwang and (409162), Jeongsu Oh and (248173), Tae-Kyung Kim and (409163), Byung Kwon Kim and (409164), Dong Su Yu and (409165), Bo Kyeng Hou and (65405), Gustavo Caetano-Anollés and (409166), Soon Gyu Hong and (409167), Kyung Mo Kim},
journal = {Figshare},
year = {2015},
doi = {10.1371/journal.pone.0062623.g003}
}Made from the index record. Check names, capitalisation and page numbers against the paper. Need another style? AI for Research has over 10,000.